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Make the analysis stranded#176

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VJalili merged 3 commits intoGenometric:devfrom
VJalili:strand
Oct 16, 2022
Merged

Make the analysis stranded#176
VJalili merged 3 commits intoGenometric:devfrom
VJalili:strand

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@VJalili VJalili commented Oct 16, 2022

Addresses #165

  • If the strand is not given in the input, it treats all the reads unstranded and reports . as the strand of the peaks in the output;
  • If the input peaks have strand, it processes the peaks stranded (i.e., peaks on the + strand are processed independent from those on the strand -);
  • By default it will parse strand from the 4th column (zero-based), which can be changed;
  • All the tests are updated to assert the changes, and related tests are added;
  • Update docs.

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codecov bot commented Oct 16, 2022

Codecov Report

Merging #176 (0689233) into dev (992df16) will decrease coverage by 0.30%.
The diff coverage is 90.14%.

@@            Coverage Diff             @@
##              dev     #176      +/-   ##
==========================================
- Coverage   97.44%   97.13%   -0.31%     
==========================================
  Files          43       43              
  Lines        2113     2167      +54     
==========================================
+ Hits         2059     2105      +46     
- Misses         10       13       +3     
- Partials       44       49       +5     
Impacted Files Coverage Δ
Core.Tests/SetsAndAttributes/BackgroundPeaks.cs 81.94% <23.07%> (ø)
Core.Tests/Basic/TConsensusPeaks.cs 90.54% <62.50%> (ø)
Core.Tests/PublicMembers.cs 91.48% <66.66%> (-5.68%) ⬇️
Core.Tests/SetsAndAttributes/Confirmed.cs 94.33% <66.66%> (ø)
Core.Tests/SetsAndAttributes/Discarded.cs 95.38% <71.42%> (ø)
Core.Tests/SetsAndAttributes/Stringent.cs 94.73% <71.42%> (ø)
Core.Tests/SetsAndAttributes/Weak.cs 94.73% <71.42%> (ø)
Core.Tests/Basic/AdjPValue.cs 100.00% <100.00%> (ø)
Core.Tests/Basic/C.cs 100.00% <100.00%> (ø)
Core.Tests/Basic/ColocalizationCount.cs 100.00% <100.00%> (ø)
... and 14 more

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